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Merge pull request #135 from mc2-center/visium-model
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10X Visium model integration
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@aditigopalan
aditigopalan authored Aug 29, 2024
2 parents e1e707f + 267d7a5 commit aee7c84
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337 changes: 213 additions & 124 deletions all_valid_values.csv
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Expand Up @@ -1645,128 +1645,6 @@ ed_hazard,Flashing,
ed_hazard,Motion,
ed_hazard,Simulation,
ed_hazard,Sound,
tool_format,Alignment Format,
tool_format,Alignment Format (Pair Only),
tool_format,Alignment Format (Text),
tool_format,Annotated Text Format,
tool_format,Antimony,
tool_format,BAM,
tool_format,BCF,
tool_format,BED,
tool_format,BLAST Results,
tool_format,BNGL,
tool_format,Binary Format,
tool_format,Biological Model Format,
tool_format,Biological Pathway Or Network Format,
tool_format,CSV,
tool_format,Chemical Data Format,
tool_format,Cytoband Format,
tool_format,Cytoscape Input File Format,
tool_format,DCC,
tool_format,DCD,
tool_format,DSV,
tool_format,Database Hits (Sequence) Format ,
tool_format,Docker Image Format,
tool_format,Document Format,
tool_format,Dot-Bracket Format,
tool_format,FASTA,
tool_format,FASTQ,
tool_format,FASTQ-Illumina,
tool_format,FCS,
tool_format,GCT/Res Format,
tool_format,GFF,
tool_format,GFF3,
tool_format,GIF,
tool_format,GML,
tool_format,GTF,
tool_format,Gene Annotation Format,
tool_format,Gene Cluster Format,
tool_format,Gene Expression Report Format,
tool_format,Genotype And Phenotype Annotation Format,
tool_format,Graph Format,
tool_format,H5AD,
tool_format,HDF,
tool_format,HDF5,
tool_format,HTML,
tool_format,Hidden Markov Model Format,
tool_format,Image Format,
tool_format,Individual Genetic Data Format,
tool_format,JPG,
tool_format,JSON,
tool_format,LSM,
tool_format,MAF,
tool_format,MAGE-ML,
tool_format,MAGE-TAB,
tool_format,MAT,
tool_format,MATLAB Script,
tool_format,MSF,
tool_format,Map Format,
tool_format,Mass Spectrometry Data Format,
tool_format,Matrix Format,
tool_format,NIFTI Format,
tool_format,Nexus Format,
tool_format,Not Applicable,
tool_format,NumPy Format,
tool_format,OME-TIFF,
tool_format,Ontology Format,
tool_format,PDF,
tool_format,PNG,
tool_format,PS,
tool_format,PSF,
tool_format,Phylip Format,
tool_format,Phylip Format Variant,
tool_format,Phylogenetic Tree Format,
tool_format,Phylogenetic Tree Format (Text),
tool_format,Protein Interaction Format,
tool_format,Python Script,
tool_format,R File Format,
tool_format,R Script,
tool_format,RDS,
tool_format,RNA Annotation Format,
tool_format,RNA Secondary Structure Format,
tool_format,RPKM,
tool_format,Raw Sequence Format,
tool_format,SAM,
tool_format,SBML,
tool_format,SQLite Format,
tool_format,SVG,
tool_format,Scores Format,
tool_format,Sequence Annotation Track Format,
tool_format,Sequence Cluster Format,
tool_format,Sequence Cluster Format (Protein),
tool_format,Sequence Feature Annotation Format,
tool_format,Sequence Feature Table Format,
tool_format,Sequence Feature Table Format (Text),
tool_format,Sequence Profile Format,
tool_format,Sequence Range Format,
tool_format,Sequence Record Format,
tool_format,Sequence Trace Format,
tool_format,Sequence Variation Annotation Format,
tool_format,TIFF,
tool_format,TSV,
tool_format,TXT,
tool_format,Tertiary Structure Format,
tool_format,Textual Format,
tool_format,Topology Format,
tool_format,Trajectory Format,
tool_format,VCF,
tool_format,Workflow Format,
tool_format,XML,
tool_format,YAML,
tool_format,bedgraph,
tool_format,bigWig,
tool_format,cel,
tool_format,imzML Metadata File,
tool_format,mzML,
tool_format,nii,
tool_format,pkl,
tool_format,sif,
tool_format,xls,
tool_format,xlsx,
tool_format,PDB,
tool_format,HED,
tool_format,MRC,
tool_format,Unspecified,
assayType,RNA nCounter,
assayType,Protein nCounter,
assayType,Protein NGS,
Expand Down Expand Up @@ -2193,6 +2071,69 @@ project_type,Core,
project_type,Project,
publication_accessibility,Open Access,
publication_accessibility,Restricted Access,
seqPlatform,Illumina Next Seq 500,
seqPlatform,Illumina Next Seq 550,
seqPlatform,Illumina Next Seq 2500,
seqPlatform,Illumina NovaSeq 6000,
seqPlatform,Illumina MiSeq,
seqPlatform,454 GS FLX Titanium,
seqPlatform,AB SOLiD 4,
seqPlatform,AB SOLiD 2,
seqPlatform,AB SOLiD 3,
seqPlatform,Complete Genomics,
seqPlatform,Illumina HiSeq X Ten,
seqPlatform,Illumina HiSeq X Five,
seqPlatform,Illumina Genome Analyzer II,
seqPlatform,Illumina Genome Analyzer IIx,
seqPlatform,Illumina HiSeq 2000,
seqPlatform,Illumina HiSeq 2500,
seqPlatform,Illumina HiSeq 4000,
seqPlatform,Illumina NextSeq,
seqPlatform,Ion Torrent PGM,
seqPlatform,Ion Torrent Proton,
seqPlatform,Ion Torrent S5,
seqPlatform,PacBio RS,
seqPlatform,NovaSeq 6000,
seqPlatform,NovaSeqS4,
seqPlatform,Ultima Genomics UG100,
seqPlatform,Oxford Nanopore minION,
seqPlatform,GridION,
seqPlatform,PromethION,
seqPlatform,PacBio Sequel2,
seqPlatform,Revio,
seqPlatform,Illumina NextSeq 1000,
seqPlatform,Illumina NextSeq 2000,
seqPlatform,Other,
seqPlatform,unknown,
seqPlatform,Not Reported,
readIndicator,R1,
readIndicator,R2,
readIndicator,R1&R2,
readIndicator,I1,
readIndicator,Other,
boolean,True,
boolean,False,
spatialReads,cDNA,
spatialReads,Spatial Barcode and UMI,
spatialLibrary,Smart-seq2,
spatialLibrary,Smart-SeqV4,
spatialLibrary,10xV1.0,
spatialLibrary,10xV1.1,
spatialLibrary,10xV2,
spatialLibrary,10xV3,
spatialLibrary,10xV3.1,
spatialLibrary,Drop-seq,
spatialLibrary,inDropsV2,
spatialLibrary,inDropsV3,
spatialLibrary,TruDrop,
spatialLibrary,Nextera XT,
endBias,3 Prime,
endBias,5 Prime,
endBias,Full Length Transcript,
rtPrimer,Oligo-dT,
rtPrimer,Poly-dT,
rtPrimer,Feature barcoding,
rtPrimer,Random,
tool_accessibility,Open Access,
tool_accessibility,Open Access (With Restrictions),
tool_accessibility,Restricted Access,
Expand Down Expand Up @@ -2379,6 +2320,128 @@ tool_download_type,Tool Wrapper (Galaxy),
tool_download_type,Tool Wrapper (Taverna),
tool_download_type,Tool wrapper (Other),
tool_download_type,VM Image,
tool_format,Alignment Format,
tool_format,Alignment Format (Pair Only),
tool_format,Alignment Format (Text),
tool_format,Annotated Text Format,
tool_format,Antimony,
tool_format,BAM,
tool_format,BCF,
tool_format,BED,
tool_format,BLAST Results,
tool_format,BNGL,
tool_format,Binary Format,
tool_format,Biological Model Format,
tool_format,Biological Pathway Or Network Format,
tool_format,CSV,
tool_format,Chemical Data Format,
tool_format,Cytoband Format,
tool_format,Cytoscape Input File Format,
tool_format,DCC,
tool_format,DCD,
tool_format,DSV,
tool_format,Database Hits (Sequence) Format ,
tool_format,Docker Image Format,
tool_format,Document Format,
tool_format,Dot-Bracket Format,
tool_format,FASTA,
tool_format,FASTQ,
tool_format,FASTQ-Illumina,
tool_format,FCS,
tool_format,GCT/Res Format,
tool_format,GFF,
tool_format,GFF3,
tool_format,GIF,
tool_format,GML,
tool_format,GTF,
tool_format,Gene Annotation Format,
tool_format,Gene Cluster Format,
tool_format,Gene Expression Report Format,
tool_format,Genotype And Phenotype Annotation Format,
tool_format,Graph Format,
tool_format,H5AD,
tool_format,HDF,
tool_format,HDF5,
tool_format,HTML,
tool_format,Hidden Markov Model Format,
tool_format,Image Format,
tool_format,Individual Genetic Data Format,
tool_format,JPG,
tool_format,JSON,
tool_format,LSM,
tool_format,MAF,
tool_format,MAGE-ML,
tool_format,MAGE-TAB,
tool_format,MAT,
tool_format,MATLAB Script,
tool_format,MSF,
tool_format,Map Format,
tool_format,Mass Spectrometry Data Format,
tool_format,Matrix Format,
tool_format,NIFTI Format,
tool_format,Nexus Format,
tool_format,Not Applicable,
tool_format,NumPy Format,
tool_format,OME-TIFF,
tool_format,Ontology Format,
tool_format,PDF,
tool_format,PNG,
tool_format,PS,
tool_format,PSF,
tool_format,Phylip Format,
tool_format,Phylip Format Variant,
tool_format,Phylogenetic Tree Format,
tool_format,Phylogenetic Tree Format (Text),
tool_format,Protein Interaction Format,
tool_format,Python Script,
tool_format,R File Format,
tool_format,R Script,
tool_format,RDS,
tool_format,RNA Annotation Format,
tool_format,RNA Secondary Structure Format,
tool_format,RPKM,
tool_format,Raw Sequence Format,
tool_format,SAM,
tool_format,SBML,
tool_format,SQLite Format,
tool_format,SVG,
tool_format,Scores Format,
tool_format,Sequence Annotation Track Format,
tool_format,Sequence Cluster Format,
tool_format,Sequence Cluster Format (Protein),
tool_format,Sequence Feature Annotation Format,
tool_format,Sequence Feature Table Format,
tool_format,Sequence Feature Table Format (Text),
tool_format,Sequence Profile Format,
tool_format,Sequence Range Format,
tool_format,Sequence Record Format,
tool_format,Sequence Trace Format,
tool_format,Sequence Variation Annotation Format,
tool_format,TIFF,
tool_format,TSV,
tool_format,TXT,
tool_format,Tertiary Structure Format,
tool_format,Textual Format,
tool_format,Topology Format,
tool_format,Trajectory Format,
tool_format,VCF,
tool_format,Workflow Format,
tool_format,XML,
tool_format,YAML,
tool_format,bedgraph,
tool_format,bigWig,
tool_format,cel,
tool_format,imzML Metadata File,
tool_format,mzML,
tool_format,nii,
tool_format,pkl,
tool_format,sif,
tool_format,xls,
tool_format,xlsx,
tool_format,PDB,
tool_format,HED,
tool_format,MRC,
tool_format,Unspecified,
tool_language,AWK,
tool_language,ActionScript,
tool_language,Ada,
Expand Down Expand Up @@ -2712,8 +2775,6 @@ tool_type,Web Application,
tool_type,Web Service,
tool_type,Workbench,
tool_type,Workflow,
boolean,True,
boolean,False,
entity_role,Developer,
entity_role,Maintainer,
entity_role,Provider,
Expand All @@ -2727,3 +2788,31 @@ entity_type,Division,
entity_type,Institute,
entity_type,Research Consortium,
entity_type,Funding Agency,
captureArea,A,
captureArea,B,
captureArea,C,
captureArea,D,
captureArea,A1,
captureArea,B1,
captureArea,C1,
captureArea,D1,
slideVersion,V1,
slideVersion,V2,
slideVersion,V3,
slideVersion,V4,
visiumFileType,reference png,
visiumFileType,reference jpg,
visiumFileType,json scale factors,
visiumFileType,probe dataset csv,
visiumFileType,qc result html,
visiumFileType,filtered mex,
visiumFileType,unfiltered mex,
visiumFileType,tissue_positions,
visiumFileType,barcodes,
visiumFileType,features,
visiumFileType,fiducial image png,
visiumFileType,fiducial image jpg,
visiumFileType,detected image png,
visiumFileType,detected jpg,
visiumFileType,high res image,
visiumFileType,low res image,
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